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ChangeLog
View file @ aeb8b8b5
Stacks 2.41 - July 8, 2019
--------------------------
Feature: populations: calculates haplotype-based Dxy (Nei, 1987) and provides for smoothing if a
reference genome is available.
Feature: populations: re-implemented full sequence export for phylip format, including partitioning information.
Stacks 2.4 - May 9, 2019
------------------------
Feature: populations: re-implemented HZAR export.
Feature: added reporting code to detect issues with inconsistent versions of libz on a host system
causing Stacks components to fail to open compressed files.
Feature: gstacks: improved PCR duplicate reporting to be per-sample.
Bugfix: populations: fixed an issues where the basepair position of a small number of loci was reported
incorrectly -- they were shifted by a small, fixed offset.
Stacks 2.3 - Jan 11, 2019
--------------------------
Feature: populations: Backwards-compatibly worked on filtering options; added long names for -r and -p and
added --min-samples-overall and --filter-haplotype-wise.
Feature: populations: Implemented --treemix.
Feature: gstacks: Improved RAD-loci reference sequences around the end of forward (restriction site-bound) reads.
Feature: gstacks: Improved the way 2-microsatelittes are dealt with.
Feature: gstacks: Changed the default value for --var-alpha from 0.05 to 0.01 (--gt-alpha is unchanged at 0.05).
Feature: gstacks: Improved PCR duplicates-related log information (distribution of clone sizes).
Feature: gstacks: Added an option to save read alignments (--write-alignments).
Feature: Backwards-compatibly switched to hyphens in command line options (underscores remain accepted
where they previously were).
Feature: cstacks/sstacks now report an error when the disk becomes full.
2.3b - Jan 23, 2019
----------
Bugfix: Fixed some limit cases causing an abort at gstacks.cc:1752.
Bugfix: Fixed some limit cases causing an abort at debruijn.cc:60.
Bugfix: Fixed some limit cases apparently causing an infinite loop in the de Bruijn code.
Bugfix: Restored compilation with the oldest C++11 GCC versions (4.9 and 5.0).
2.3c - Feb 27, 2019
---------
Bugfix: Fixed assert failure at gstacks.cc:1171 (corrected with a return on gstacks.cc:1126)
Bugfix: inadvertantly compiling out BAM support from process_radtags due to the removal of the HAVE_BAM
config option, which occurred when we moved the BAM library internally to Stacks.
Bugfix: corrected infinite loop in populations when --write-single-snp and -r were enabled.
Bugfix: correct missing comment marker in population's FASTA exports and missing ']' character in FASTA comments.
2.3d - Feb 28, 2019
---------
Bugfix: the snps_per_loc_postfilters distribution in the populations.log.distrib file was slightly off due to counting
the number of SNPs at loci where despite SNP objects present at the locus, all sites were fixed in the
focal populations.
Bugfix: Some haplotypes could pass through the filter, even after particular SNPs were filtered from them.
Bufgix: Corrected the samples per locus and absent-samples per locus distributions from populations.
2.3e - Mar 20, 2019
---------
Bugfix: the --write-random-snp flag was causing an infinite loop in populations.
Stacks 2.2 - Aug 22, 2018
--------------------------
Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed
before they are processed.
Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces
--min-kmer-freq which is now deprecated
Bugfix: Fixed a breaking circumstantial segmentation fault in populations
Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.
Stacks 2.1 - June 25, 2018
......
Makefile.am
View file @ aeb8b8b5
......@@ -89,22 +89,11 @@ dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \
dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \
php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php \
php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php \
php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php \
php/stacks_functions.php php/view_sequence.php php/sequence_blast.php \
php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php \
php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css \
php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png \
php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png \
php/images/stacks_logo_rev_small.png
LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh
TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t
EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
EXTRA_DIST = LICENSE INSTALL README ChangeLog $(TESTS)
pkglocalstatedir = $(localstatedir)/$(PACKAGE)
......@@ -118,11 +107,6 @@ install-data-hook:
sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
chmod +x $(DESTDIR)$(bindir)/ref_map.pl
sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst
mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist
echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php
$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export
sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
......
Makefile.in
View file @ aeb8b8b5
# Makefile.in generated by automake 1.15 from Makefile.am.
# Makefile.in generated by automake 1.13.4 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2014 Free Software Foundation, Inc.
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -16,19 +16,8 @@
VPATH = @srcdir@
am__is_gnu_make = { \
if test -z '$(MAKELEVEL)'; then \
false; \
elif test -n '$(MAKE_HOST)'; then \
true; \
elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
true; \
else \
false; \
fi; \
}
am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
......@@ -95,14 +84,20 @@ bin_PROGRAMS = ustacks$(EXEEXT) cstacks$(EXEEXT) sstacks$(EXEEXT) \
populations$(EXEEXT) phasedstacks$(EXEEXT) tsv2bam$(EXEEXT) \
gstacks$(EXEEXT)
subdir = .
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/configure $(am__configure_deps) \
$(srcdir)/config.h.in $(dist_bin_SCRIPTS) \
$(dist_noinst_SCRIPTS) $(top_srcdir)/config/depcomp \
$(top_srcdir)/config/test-driver ChangeLog INSTALL README \
config/ar-lib config/compile config/depcomp config/install-sh \
config/missing $(top_srcdir)/config/ar-lib \
$(top_srcdir)/config/compile $(top_srcdir)/config/install-sh \
$(top_srcdir)/config/missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
$(am__configure_deps) $(dist_bin_SCRIPTS) \
$(dist_noinst_SCRIPTS) $(am__DIST_COMMON)
am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
configure.lineno config.status.lineno
mkinstalldirs = $(install_sh) -d
......@@ -142,8 +137,7 @@ am_libpop_a_OBJECTS = src/export_formats.$(OBJEXT) \
src/genotype_dictionaries.$(OBJEXT) src/PopSum.$(OBJEXT) \
src/Hwp.$(OBJEXT)
libpop_a_OBJECTS = $(am_libpop_a_OBJECTS)
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
"$(DESTDIR)$(pkgdatadir)"
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"
PROGRAMS = $(bin_PROGRAMS)
am_clone_filter_OBJECTS = src/clone_filter.$(OBJEXT)
clone_filter_OBJECTS = $(am_clone_filter_OBJECTS)
......@@ -279,7 +273,6 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
DATA = $(nobase_pkgdata_DATA)
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
am__recursive_targets = \
......@@ -485,12 +478,6 @@ TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/config/test-driver
TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
$(TEST_LOG_FLAGS)
DIST_SUBDIRS = $(SUBDIRS)
am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
$(top_srcdir)/config/ar-lib $(top_srcdir)/config/compile \
$(top_srcdir)/config/depcomp $(top_srcdir)/config/install-sh \
$(top_srcdir)/config/missing $(top_srcdir)/config/test-driver \
ChangeLog INSTALL README config/ar-lib config/compile \
config/depcomp config/install-sh config/missing
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
......@@ -621,7 +608,6 @@ pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
runstatedir = @runstatedir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
......@@ -710,20 +696,9 @@ dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \
scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb # scripts/denovo_map.py
dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \
php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php \
php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php \
php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php \
php/stacks_functions.php php/view_sequence.php php/sequence_blast.php \
php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php \
php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css \
php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png \
php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png \
php/images/stacks_logo_rev_small.png
LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh
TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t
EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
EXTRA_DIST = LICENSE INSTALL README ChangeLog $(TESTS)
pkglocalstatedir = $(localstatedir)/$(PACKAGE)
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-recursive
......@@ -745,6 +720,7 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --foreign Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
......@@ -765,8 +741,8 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
@test -f $@ || rm -f stamp-h1
@test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
@if test ! -f $@; then rm -f stamp-h1; else :; fi
@if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
......@@ -1066,30 +1042,6 @@ distclean-compile:
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
install-nobase_pkgdataDATA: $(nobase_pkgdata_DATA)
@$(NORMAL_INSTALL)
@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)'"; \
$(MKDIR_P) "$(DESTDIR)$(pkgdatadir)" || exit 1; \
fi; \
$(am__nobase_list) | while read dir files; do \
xfiles=; for file in $$files; do \
if test -f "$$file"; then xfiles="$$xfiles $$file"; \
else xfiles="$$xfiles $(srcdir)/$$file"; fi; done; \
test -z "$$xfiles" || { \
test "x$$dir" = x. || { \
echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
$(MKDIR_P) "$(DESTDIR)$(pkgdatadir)/$$dir"; }; \
echo " $(INSTALL_DATA) $$xfiles '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
$(INSTALL_DATA) $$xfiles "$(DESTDIR)$(pkgdatadir)/$$dir" || exit $$?; }; \
done
uninstall-nobase_pkgdataDATA:
@$(NORMAL_UNINSTALL)
@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \
$(am__nobase_strip_setup); files=`$(am__nobase_strip)`; \
dir='$(DESTDIR)$(pkgdatadir)'; $(am__uninstall_files_from_dir)
# This directory's subdirectories are mostly independent; you can cd
# into them and run 'make' without going through this Makefile.
......@@ -1227,7 +1179,7 @@ $(TEST_SUITE_LOG): $(TEST_LOGS)
if test -n "$$am__remaking_logs"; then \
echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \
"recursion detected" >&2; \
elif test -n "$$redo_logs"; then \
else \
am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \
fi; \
if $(am__make_dryrun); then :; else \
......@@ -1462,16 +1414,10 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
@echo WARNING: "Support for distribution archives compressed with" \
"legacy program 'compress' is deprecated." >&2
@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
@echo WARNING: "Support for shar distribution archives is" \
"deprecated." >&2
@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
$(am__post_remove_distdir)
......@@ -1506,17 +1452,16 @@ distcheck: dist
esac
chmod -R a-w $(distdir)
chmod u+w $(distdir)
mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
mkdir $(distdir)/_build $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
&& $(am__cd) $(distdir)/_build/sub \
&& ../../configure \
&& $(am__cd) $(distdir)/_build \
&& ../configure --srcdir=.. --prefix="$$dc_install_base" \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
--srcdir=../.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
......@@ -1572,10 +1517,10 @@ distcleancheck: distclean
check-am: all-am
$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-recursive
all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) $(DATA) config.h
all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) config.h
installdirs: installdirs-recursive
installdirs-am:
for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pkgdatadir)"; do \
for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: install-recursive
......@@ -1637,7 +1582,7 @@ info: info-recursive
info-am:
install-data-am: install-nobase_pkgdataDATA
install-data-am:
@$(NORMAL_INSTALL)
$(MAKE) $(AM_MAKEFLAGS) install-data-hook
install-dvi: install-dvi-recursive
......@@ -1685,8 +1630,7 @@ ps: ps-recursive
ps-am:
uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
uninstall-nobase_pkgdataDATA
uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS
@$(NORMAL_INSTALL)
$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
.MAKE: $(am__recursive_targets) all check-am install-am \
......@@ -1704,16 +1648,13 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
install-data-am install-data-hook install-dist_binSCRIPTS \
install-dvi install-dvi-am install-exec install-exec-am \
install-html install-html-am install-info install-info-am \
install-man install-nobase_pkgdataDATA install-pdf \
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs installdirs-am \
maintainer-clean maintainer-clean-generic mostlyclean \
mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
recheck tags tags-am uninstall uninstall-am \
uninstall-binPROGRAMS uninstall-dist_binSCRIPTS uninstall-hook \
uninstall-nobase_pkgdataDATA
.PRECIOUS: Makefile
install-man install-pdf install-pdf-am install-ps \
install-ps-am install-strip installcheck installcheck-am \
installdirs installdirs-am maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
mostlyclean-generic pdf pdf-am ps ps-am recheck tags tags-am \
uninstall uninstall-am uninstall-binPROGRAMS \
uninstall-dist_binSCRIPTS uninstall-hook
debug:
......@@ -1726,11 +1667,6 @@ install-data-hook:
sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
chmod +x $(DESTDIR)$(bindir)/ref_map.pl
sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst
mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist
echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php
$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export
sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
......
aclocal.m4
View file @ aeb8b8b5
# generated automatically by aclocal 1.15 -*- Autoconf -*-
# generated automatically by aclocal 1.13.4 -*- Autoconf -*-
# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -20,7 +20,7 @@ You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.])])
# Copyright (C) 2002-2014 Free Software Foundation, Inc.
# Copyright (C) 2002-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
[am__api_version='1.15'
[am__api_version='1.13'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
m4_if([$1], [1.15], [],
m4_if([$1], [1.13.4], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
......@@ -51,12 +51,12 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
[AM_AUTOMAKE_VERSION([1.15])dnl
[AM_AUTOMAKE_VERSION([1.13.4])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# Copyright (C) 2011-2014 Free Software Foundation, Inc.
# Copyright (C) 2011-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -76,8 +76,7 @@ AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
: ${AR=ar}
AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
[AC_LANG_PUSH([C])
am_cv_ar_interface=ar
[am_cv_ar_interface=ar
AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
[am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
AC_TRY_EVAL([am_ar_try])
......@@ -94,7 +93,7 @@ AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
fi
rm -f conftest.lib libconftest.a
])
AC_LANG_POP([C])])
])
case $am_cv_ar_interface in
ar)
......@@ -118,7 +117,7 @@ AC_SUBST([AR])dnl
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -163,14 +162,15 @@ AC_SUBST([AR])dnl
# configured tree to be moved without reconfiguration.
AC_DEFUN([AM_AUX_DIR_EXPAND],
[AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl
# Expand $ac_aux_dir to an absolute path.
am_aux_dir=`cd "$ac_aux_dir" && pwd`
[dnl Rely on autoconf to set up CDPATH properly.
AC_PREREQ([2.50])dnl
# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`
])
# AM_CONDITIONAL -*- Autoconf -*-
# Copyright (C) 1997-2014 Free Software Foundation, Inc.
# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -201,7 +201,7 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -392,7 +392,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -468,7 +468,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# Do all the work for Automake. -*- Autoconf -*-
# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -477,12 +477,6 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
m4_define([AC_PROG_CC],
m4_defn([AC_PROG_CC])
[_AM_PROG_CC_C_O
])
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
......@@ -558,8 +552,8 @@ AC_REQUIRE([AC_PROG_MKDIR_P])dnl
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
# We need awk for the "check" target (and possibly the TAP driver). The
# system "awk" is bad on some platforms.
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
......@@ -591,51 +585,6 @@ dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
AC_CONFIG_COMMANDS_PRE(dnl
[m4_provide_if([_AM_COMPILER_EXEEXT],
[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
# POSIX will say in a future version that running "rm -f" with no argument
# is OK; and we want to be able to make that assumption in our Makefile
# recipes. So use an aggressive probe to check that the usage we want is
# actually supported "in the wild" to an acceptable degree.
# See automake bug#10828.
# To make any issue more visible, cause the running configure to be aborted
# by default if the 'rm' program in use doesn't match our expectations; the
# user can still override this though.
if rm -f && rm -fr && rm -rf; then : OK; else
cat >&2 <<'END'
Oops!
Your 'rm' program seems unable to run without file operands specified
on the command line, even when the '-f' option is present. This is contrary
to the behaviour of most rm programs out there, and not conforming with
the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
Please tell bug-automake@gnu.org about your system, including the value
of your $PATH and any error possibly output before this message. This
can help us improve future automake versions.
END
if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
echo 'Configuration will proceed anyway, since you have set the' >&2
echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
echo >&2
else
cat >&2 <<'END'
Aborting the configuration process, to ensure you take notice of the issue.
You can download and install GNU coreutils to get an 'rm' implementation
that behaves properly: <http://www.gnu.org/software/coreutils/>.
If you want to complete the configuration process using your problematic
'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
to "yes", and re-run configure.
END
AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
fi
fi
dnl The trailing newline in this macro's definition is deliberate, for
dnl backward compatibility and to allow trailing 'dnl'-style comments
dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
......@@ -644,6 +593,7 @@ dnl mangled by Autoconf and run in a shell conditional statement.
m4_define([_AC_COMPILER_EXEEXT],
m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
# When config.status generates a header, we must update the stamp-h file.
# This file resides in the same directory as the config header
# that is generated. The stamp files are numbered to have different names.
......@@ -665,7 +615,7 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -676,7 +626,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
if test x"${install_sh+set}" != xset; then
if test x"${install_sh}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
......@@ -686,7 +636,7 @@ if test x"${install_sh+set}" != xset; then
fi
AC_SUBST([install_sh])])
# Copyright (C) 2003-2014 Free Software Foundation, Inc.
# Copyright (C) 2003-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -707,7 +657,7 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -755,9 +705,41 @@ AC_MSG_RESULT([$_am_result])
rm -f confinc confmf
])
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# AM_PROG_CC_C_O
# --------------
# Like AC_PROG_CC_C_O, but changed for automake.
AC_DEFUN([AM_PROG_CC_C_O],
[AC_REQUIRE([AC_PROG_CC_C_O])dnl
AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([compile])dnl
# FIXME: we rely on the cache variable name because
# there is no other way.
set dummy $CC
am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
if test "$am_t" != yes; then
# Losing compiler, so override with the script.
# FIXME: It is wrong to rewrite CC.
# But if we don't then we get into trouble of one sort or another.
# A longer-term fix would be to have automake use am__CC in this case,
# and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
CC="$am_aux_dir/compile $CC"
fi
dnl Make sure AC_PROG_CC is never called again, or it will override our
dnl setting of CC.
m4_define([AC_PROG_CC],
[m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
])
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
# Copyright (C) 1997-2014 Free Software Foundation, Inc.
# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -796,7 +778,7 @@ fi
# Helper functions for option handling. -*- Autoconf -*-
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -825,73 +807,9 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# _AM_PROG_CC_C_O
# ---------------
# Like AC_PROG_CC_C_O, but changed for automake. We rewrite AC_PROG_CC
# to automatically call this.
AC_DEFUN([_AM_PROG_CC_C_O],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([compile])dnl
AC_LANG_PUSH([C])dnl
AC_CACHE_CHECK(
[whether $CC understands -c and -o together],
[am_cv_prog_cc_c_o],
[AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
# Make sure it works both with $CC and with simple cc.
# Following AC_PROG_CC_C_O, we do the test twice because some
# compilers refuse to overwrite an existing .o file with -o,
# though they will create one.
am_cv_prog_cc_c_o=yes
for am_i in 1 2; do
if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
&& test -f conftest2.$ac_objext; then
: OK
else
am_cv_prog_cc_c_o=no
break
fi
done
rm -f core conftest*
unset am_i])
if test "$am_cv_prog_cc_c_o" != yes; then
# Losing compiler, so override with the script.
# FIXME: It is wrong to rewrite CC.
# But if we don't then we get into trouble of one sort or another.
# A longer-term fix would be to have automake use am__CC in this case,
# and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
CC="$am_aux_dir/compile $CC"
fi
AC_LANG_POP([C])])
# For backward compatibility.
AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# AM_RUN_LOG(COMMAND)
# -------------------
# Run COMMAND, save the exit status in ac_status, and log it.
# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
AC_DEFUN([AM_RUN_LOG],
[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
(exit $ac_status); }])
# Check to make sure that the build environment is sane. -*- Autoconf -*-
# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -972,7 +890,7 @@ AC_CONFIG_COMMANDS_PRE(
rm -f conftest.file
])
# Copyright (C) 2009-2014 Free Software Foundation, Inc.
# Copyright (C) 2009-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -1032,7 +950,7 @@ AC_SUBST([AM_BACKSLASH])dnl
_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
])
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -1060,7 +978,7 @@ fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
# Copyright (C) 2006-2014 Free Software Foundation, Inc.
# Copyright (C) 2006-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......@@ -1079,7 +997,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
# Copyright (C) 2004-2014 Free Software Foundation, Inc.
# Copyright (C) 2004-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
......
config.h.in
View file @ aeb8b8b5
......@@ -89,6 +89,9 @@
/* Define to 1 if the system has the type `_Bool'. */
#undef HAVE__BOOL
/* Define to 1 if your C compiler doesn't accept -c and -o together. */
#undef NO_MINUS_C_MINUS_O
/* Name of package */
#undef PACKAGE
......
config/ar-lib
View file @ aeb8b8b5
......@@ -4,7 +4,7 @@
me=ar-lib
scriptversion=2012-03-01.08; # UTC
# Copyright (C) 2010-2014 Free Software Foundation, Inc.
# Copyright (C) 2010-2013 Free Software Foundation, Inc.
# Written by Peter Rosin <peda@lysator.liu.se>.
#
# This program is free software; you can redistribute it and/or modify
......
config/compile
View file @ aeb8b8b5
......@@ -3,7 +3,7 @@
scriptversion=2012-10-14.11; # UTC
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
# Written by Tom Tromey <tromey@cygnus.com>.
#
# This program is free software; you can redistribute it and/or modify
......
config/depcomp
View file @ aeb8b8b5
......@@ -3,7 +3,7 @@
scriptversion=2013-05-30.07; # UTC
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
# Copyright (C) 1999-2013 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......
config/install-sh
View file @ aeb8b8b5
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2014-09-12.12; # UTC
scriptversion=2011-11-20.07; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
......@@ -41,15 +41,19 @@ scriptversion=2014-09-12.12; # UTC
# This script is compatible with the BSD install script, but was written
# from scratch.
tab=' '
nl='
'
IFS=" $tab$nl"
IFS=" "" $nl"
# Set DOITPROG to "echo" to test this script.
# set DOITPROG to echo to test this script
# Don't use :- since 4.3BSD and earlier shells don't like it.
doit=${DOITPROG-}
doit_exec=${doit:-exec}
if test -z "$doit"; then
doit_exec=exec
else
doit_exec=$doit
fi
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
......@@ -64,6 +68,17 @@ mvprog=${MVPROG-mv}
rmprog=${RMPROG-rm}
stripprog=${STRIPPROG-strip}
posix_glob='?'
initialize_posix_glob='
test "$posix_glob" != "?" || {
if (set -f) 2>/dev/null; then
posix_glob=
else
posix_glob=:
fi
}
'
posix_mkdir=
# Desired mode of installed file.
......@@ -82,7 +97,7 @@ dir_arg=
dst_arg=
copy_on_change=false
is_target_a_directory=possibly
no_target_directory=
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
......@@ -128,7 +143,8 @@ while test $# -ne 0; do
-m) mode=$2
case $mode in
*' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
*' '* | *' '* | *'
'* | *'*'* | *'?'* | *'['*)
echo "$0: invalid mode: $mode" >&2
exit 1;;
esac
......@@ -139,16 +155,14 @@ while test $# -ne 0; do
-s) stripcmd=$stripprog;;
-t)
is_target_a_directory=always
dst_arg=$2
-t) dst_arg=$2
# Protect names problematic for 'test' and other utilities.
case $dst_arg in
-* | [=\(\)!]) dst_arg=./$dst_arg;;
esac
shift;;
-T) is_target_a_directory=never;;
-T) no_target_directory=true;;
--version) echo "$0 $scriptversion"; exit $?;;
......@@ -163,16 +177,6 @@ while test $# -ne 0; do
shift
done
# We allow the use of options -d and -T together, by making -d
# take the precedence; this is for compatibility with GNU install.
if test -n "$dir_arg"; then
if test -n "$dst_arg"; then
echo "$0: target directory not allowed when installing a directory." >&2
exit 1
fi
fi
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
......@@ -203,15 +207,6 @@ if test $# -eq 0; then
exit 0
fi
if test -z "$dir_arg"; then
if test $# -gt 1 || test "$is_target_a_directory" = always; then
if test ! -d "$dst_arg"; then
echo "$0: $dst_arg: Is not a directory." >&2
exit 1
fi
fi
fi
if test -z "$dir_arg"; then
do_exit='(exit $ret); exit $ret'
trap "ret=129; $do_exit" 1
......@@ -274,7 +269,7 @@ do
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
if test "$is_target_a_directory" = never; then
if test -n "$no_target_directory"; then
echo "$0: $dst_arg: Is a directory" >&2
exit 1
fi
......@@ -282,7 +277,33 @@ do
dst=$dstdir/`basename "$src"`
dstdir_status=0
else
dstdir=`dirname "$dst"`
# Prefer dirname, but fall back on a substitute if dirname fails.
dstdir=`
(dirname "$dst") 2>/dev/null ||
expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$dst" : 'X\(//\)[^/]' \| \
X"$dst" : 'X\(//\)$' \| \
X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$dst" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
}
/^X\(\/\/\)[^/].*/{
s//\1/
q
}
/^X\(\/\/\)$/{
s//\1/
q
}
/^X\(\/\).*/{
s//\1/
q
}
s/.*/./; q'
`
test -d "$dstdir"
dstdir_status=$?
fi
......@@ -324,41 +345,34 @@ do
# is incompatible with FreeBSD 'install' when (umask & 300) != 0.
;;
*)
# $RANDOM is not portable (e.g. dash); use it when possible to
# lower collision chance
tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
trap 'ret=$?; rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir" 2>/dev/null; exit $ret' 0
trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
# As "mkdir -p" follows symlinks and we work in /tmp possibly; so
# create the $tmpdir first (and fail if unsuccessful) to make sure
# that nobody tries to guess the $tmpdir name.
if (umask $mkdir_umask &&
$mkdirprog $mkdir_mode "$tmpdir" &&
exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
then
if test -z "$dir_arg" || {
# Check for POSIX incompatibilities with -m.
# HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
# other-writable bit of parent directory when it shouldn't.
# FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
test_tmpdir="$tmpdir/a"
ls_ld_tmpdir=`ls -ld "$test_tmpdir"`
ls_ld_tmpdir=`ls -ld "$tmpdir"`
case $ls_ld_tmpdir in
d????-?r-*) different_mode=700;;
d????-?--*) different_mode=755;;
*) false;;
esac &&
$mkdirprog -m$different_mode -p -- "$test_tmpdir" && {
ls_ld_tmpdir_1=`ls -ld "$test_tmpdir"`
$mkdirprog -m$different_mode -p -- "$tmpdir" && {
ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
}
}
then posix_mkdir=:
fi
rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
rmdir "$tmpdir/d" "$tmpdir"
else
# Remove any dirs left behind by ancient mkdir implementations.
rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 2>/dev/null
rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
fi
trap '' 0;;
esac;;
......@@ -382,12 +396,14 @@ do
*) prefix='';;
esac
eval "$initialize_posix_glob"
oIFS=$IFS
IFS=/
set -f
$posix_glob set -f
set fnord $dstdir
shift
set +f
$posix_glob set +f
IFS=$oIFS
prefixes=
......@@ -458,10 +474,13 @@ do
if $copy_on_change &&
old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
set -f &&
eval "$initialize_posix_glob" &&
$posix_glob set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
set +f &&
$posix_glob set +f &&
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
......
config/missing
View file @ aeb8b8b5
#! /bin/sh
# Common wrapper for a few potentially missing GNU programs.
scriptversion=2013-10-28.13; # UTC
scriptversion=2012-06-26.16; # UTC
# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# This program is free software; you can redistribute it and/or modify
......@@ -160,7 +160,7 @@ give_advice ()
;;
autom4te*)
echo "You might have modified some maintainer files that require"
echo "the 'autom4te' program to be rebuilt."
echo "the 'automa4te' program to be rebuilt."
program_details 'autom4te'
;;
bison*|yacc*)
......
config/test-driver
View file @ aeb8b8b5
#! /bin/sh
# test-driver - basic testsuite driver script.
scriptversion=2013-07-13.22; # UTC
scriptversion=2012-06-27.10; # UTC
# Copyright (C) 2011-2014 Free Software Foundation, Inc.
# Copyright (C) 2011-2013 Free Software Foundation, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......@@ -44,12 +44,13 @@ print_usage ()
Usage:
test-driver --test-name=NAME --log-file=PATH --trs-file=PATH
[--expect-failure={yes|no}] [--color-tests={yes|no}]
[--enable-hard-errors={yes|no}] [--]
TEST-SCRIPT [TEST-SCRIPT-ARGUMENTS]
[--enable-hard-errors={yes|no}] [--] TEST-SCRIPT
The '--test-name', '--log-file' and '--trs-file' options are mandatory.
END
}
# TODO: better error handling in option parsing (in particular, ensure
# TODO: $log_file, $trs_file and $test_name are defined).
test_name= # Used for reporting.
log_file= # Where to save the output of the test script.
trs_file= # Where to save the metadata of the test run.
......@@ -68,23 +69,10 @@ while test $# -gt 0; do
--enable-hard-errors) enable_hard_errors=$2; shift;;
--) shift; break;;
-*) usage_error "invalid option: '$1'";;
*) break;;
esac
shift
done
missing_opts=
test x"$test_name" = x && missing_opts="$missing_opts --test-name"
test x"$log_file" = x && missing_opts="$missing_opts --log-file"
test x"$trs_file" = x && missing_opts="$missing_opts --trs-file"
if test x"$missing_opts" != x; then
usage_error "the following mandatory options are missing:$missing_opts"
fi
if test $# -eq 0; then
usage_error "missing argument"
fi
if test $color_tests = yes; then
# Keep this in sync with 'lib/am/check.am:$(am__tty_colors)'.
red='' # Red.
......@@ -106,14 +94,11 @@ trap "st=143; $do_exit" 15
# Test script is run here.
"$@" >$log_file 2>&1
estatus=$?
if test $enable_hard_errors = no && test $estatus -eq 99; then
tweaked_estatus=1
else
tweaked_estatus=$estatus
estatus=1
fi
case $tweaked_estatus:$expect_failure in
case $estatus:$expect_failure in
0:yes) col=$red res=XPASS recheck=yes gcopy=yes;;
0:*) col=$grn res=PASS recheck=no gcopy=no;;
77:*) col=$blu res=SKIP recheck=no gcopy=yes;;
......@@ -122,12 +107,6 @@ case $tweaked_estatus:$expect_failure in
*:*) col=$red res=FAIL recheck=yes gcopy=yes;;
esac
# Report the test outcome and exit status in the logs, so that one can
# know whether the test passed or failed simply by looking at the '.log'
# file, without the need of also peaking into the corresponding '.trs'
# file (automake bug#11814).
echo "$res $test_name (exit status: $estatus)" >>$log_file
# Report outcome to console.
echo "${col}${res}${std}: $test_name"
......
configure
View file @ aeb8b8b5
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for Stacks 2.2.
# Generated by GNU Autoconf 2.69 for Stacks 2.41.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
......@@ -577,8 +577,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='Stacks'
PACKAGE_TARNAME='stacks'
PACKAGE_VERSION='2.2'
PACKAGE_STRING='Stacks 2.2'
PACKAGE_VERSION='2.41'
PACKAGE_STRING='Stacks 2.41'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
......@@ -701,7 +701,6 @@ infodir
docdir
oldincludedir
includedir
runstatedir
localstatedir
sharedstatedir
sysconfdir
......@@ -778,7 +777,6 @@ datadir='${datarootdir}'
sysconfdir='${prefix}/etc'
sharedstatedir='${prefix}/com'
localstatedir='${prefix}/var'
runstatedir='${localstatedir}/run'
includedir='${prefix}/include'
oldincludedir='/usr/include'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
......@@ -1031,15 +1029,6 @@ do
| -silent | --silent | --silen | --sile | --sil)
silent=yes ;;
-runstatedir | --runstatedir | --runstatedi | --runstated \
| --runstate | --runstat | --runsta | --runst | --runs \
| --run | --ru | --r)
ac_prev=runstatedir ;;
-runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
| --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
| --run=* | --ru=* | --r=*)
runstatedir=$ac_optarg ;;
-sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
ac_prev=sbindir ;;
-sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
......@@ -1177,7 +1166,7 @@ fi
for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
datadir sysconfdir sharedstatedir localstatedir includedir \
oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
libdir localedir mandir runstatedir
libdir localedir mandir
do
eval ac_val=\$$ac_var
# Remove trailing slashes.
......@@ -1290,7 +1279,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures Stacks 2.2 to adapt to many kinds of systems.
\`configure' configures Stacks 2.41 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
......@@ -1330,7 +1319,6 @@ Fine tuning of the installation directories:
--sysconfdir=DIR read-only single-machine data [PREFIX/etc]
--sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
--localstatedir=DIR modifiable single-machine data [PREFIX/var]
--runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run]
--libdir=DIR object code libraries [EPREFIX/lib]
--includedir=DIR C header files [PREFIX/include]
--oldincludedir=DIR C header files for non-gcc [/usr/include]
......@@ -1357,7 +1345,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of Stacks 2.2:";;
short | recursive ) echo "Configuration of Stacks 2.41:";;
esac
cat <<\_ACEOF
......@@ -1451,7 +1439,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
Stacks configure 2.2
Stacks configure 2.41
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -1950,7 +1938,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by Stacks $as_me 2.2, which was
It was created by Stacks $as_me 2.41, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
......@@ -2327,7 +2315,7 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
am__api_version='1.15'
am__api_version='1.13'
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
......@@ -2499,8 +2487,8 @@ test "$program_suffix" != NONE &&
ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
# Expand $ac_aux_dir to an absolute path.
am_aux_dir=`cd "$ac_aux_dir" && pwd`
# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`
if test x"${MISSING+set}" != xset; then
case $am_aux_dir in
......@@ -2519,7 +2507,7 @@ else
$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
fi
if test x"${install_sh+set}" != xset; then
if test x"${install_sh}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
......@@ -2813,7 +2801,7 @@ fi
# Define the identity of the package.
PACKAGE='stacks'
VERSION='2.2'
VERSION='2.41'
cat >>confdefs.h <<_ACEOF
......@@ -2847,8 +2835,8 @@ MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
mkdir_p='$(MKDIR_P)'
# We need awk for the "check" target (and possibly the TAP driver). The
# system "awk" is bad on some platforms.
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
# Always define AMTAR for backward compatibility. Yes, it's still used
# in the wild :-( We should find a proper way to deprecate it ...
AMTAR='$${TAR-tar}'
......@@ -2864,48 +2852,6 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
# POSIX will say in a future version that running "rm -f" with no argument
# is OK; and we want to be able to make that assumption in our Makefile
# recipes. So use an aggressive probe to check that the usage we want is
# actually supported "in the wild" to an acceptable degree.
# See automake bug#10828.
# To make any issue more visible, cause the running configure to be aborted
# by default if the 'rm' program in use doesn't match our expectations; the
# user can still override this though.
if rm -f && rm -fr && rm -rf; then : OK; else
cat >&2 <<'END'
Oops!
Your 'rm' program seems unable to run without file operands specified
on the command line, even when the '-f' option is present. This is contrary
to the behaviour of most rm programs out there, and not conforming with
the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
Please tell bug-automake@gnu.org about your system, including the value
of your $PATH and any error possibly output before this message. This
can help us improve future automake versions.
END
if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
echo 'Configuration will proceed anyway, since you have set the' >&2
echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
echo >&2
else
cat >&2 <<'END'
Aborting the configuration process, to ensure you take notice of the issue.
You can download and install GNU coreutils to get an 'rm' implementation
that behaves properly: <http://www.gnu.org/software/coreutils/>.
If you want to complete the configuration process using your problematic
'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
to "yes", and re-run configure.
END
as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
fi
fi
ac_config_headers="$ac_config_headers config.h"
......@@ -4163,65 +4109,6 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
if ${am_cv_prog_cc_c_o+:} false; then :
$as_echo_n "(cached) " >&6
else
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
main ()
{
;
return 0;
}
_ACEOF
# Make sure it works both with $CC and with simple cc.
# Following AC_PROG_CC_C_O, we do the test twice because some
# compilers refuse to overwrite an existing .o file with -o,
# though they will create one.
am_cv_prog_cc_c_o=yes
for am_i in 1 2; do
if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } \
&& test -f conftest2.$ac_objext; then
: OK
else
am_cv_prog_cc_c_o=no
break
fi
done
rm -f core conftest*
unset am_i
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
$as_echo "$am_cv_prog_cc_c_o" >&6; }
if test "$am_cv_prog_cc_c_o" != yes; then
# Losing compiler, so override with the script.
# FIXME: It is wrong to rewrite CC.
# But if we don't then we get into trouble of one sort or another.
# A longer-term fix would be to have automake use am__CC in this case,
# and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
CC="$am_aux_dir/compile $CC"
fi
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
depcc="$CC" am_compiler_list=
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
......@@ -4350,6 +4237,131 @@ else
fi
if test "x$CC" != xcc; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC and cc understand -c and -o together" >&5
$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether cc understands -c and -o together" >&5
$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
fi
set dummy $CC; ac_cc=`$as_echo "$2" |
sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
if eval \${ac_cv_prog_cc_${ac_cc}_c_o+:} false; then :
$as_echo_n "(cached) " >&6
else
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
main ()
{
;
return 0;
}
_ACEOF
# Make sure it works both with $CC and with simple cc.
# We do the test twice because some compilers refuse to overwrite an
# existing .o file with -o, though they will create one.
ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
rm -f conftest2.*
if { { case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
$as_echo "$ac_try_echo"; } >&5
(eval "$ac_try") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; } &&
test -f conftest2.$ac_objext && { { case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
$as_echo "$ac_try_echo"; } >&5
(eval "$ac_try") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; };
then
eval ac_cv_prog_cc_${ac_cc}_c_o=yes
if test "x$CC" != xcc; then
# Test first that cc exists at all.
if { ac_try='cc -c conftest.$ac_ext >&5'
{ { case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
$as_echo "$ac_try_echo"; } >&5
(eval "$ac_try") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; }; then
ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
rm -f conftest2.*
if { { case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
$as_echo "$ac_try_echo"; } >&5
(eval "$ac_try") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; } &&
test -f conftest2.$ac_objext && { { case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
$as_echo "$ac_try_echo"; } >&5
(eval "$ac_try") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; };
then
# cc works too.
:
else
# cc exists but doesn't like -o.
eval ac_cv_prog_cc_${ac_cc}_c_o=no
fi
fi
fi
else
eval ac_cv_prog_cc_${ac_cc}_c_o=no
fi
rm -f core conftest*
fi
if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
$as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h
fi
# FIXME: we rely on the cache variable name because
# there is no other way.
set dummy $CC
am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
if test "$am_t" != yes; then
# Losing compiler, so override with the script.
# FIXME: It is wrong to rewrite CC.
# But if we don't then we get into trouble of one sort or another.
# A longer-term fix would be to have automake use am__CC in this case,
# and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
CC="$am_aux_dir/compile $CC"
fi
ax_cxx_compile_cxx11_required=true
......@@ -5532,12 +5544,6 @@ $as_echo_n "checking the archiver ($AR) interface... " >&6; }
if ${am_cv_ar_interface+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
am_cv_ar_interface=ar
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
......@@ -5569,11 +5575,6 @@ if ac_fn_c_try_compile "$LINENO"; then :
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_ar_interface" >&5
......@@ -7416,7 +7417,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by Stacks $as_me 2.2, which was
This file was extended by Stacks $as_me 2.41, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
......@@ -7482,7 +7483,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
Stacks config.status 2.2
Stacks config.status 2.41
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
......
configure.ac
View file @ aeb8b8b5
......@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
AC_INIT([Stacks], [2.2])
AC_INIT([Stacks], [2.41])
AC_CONFIG_AUX_DIR([config])
AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
AC_CONFIG_SRCDIR([src/ustacks.cc])
......
debian/NEWS.Debian 0 → 100644
View file @ aeb8b8b5
stacks (2.41+dfsg-1) unstable; urgency=medium
* Removed stacks-web package since the code for the web service
was removed from upstream source and the package has no active
users according to popcon anyway
-- Andreas Tille <tille@debian.org> Wed, 10 Jul 2019 21:58:30 +0200
debian/apache2-conf/stacks-web.conf deleted 100644 → 0
View file @ 1aaba5f8
Alias /stacks /usr/share/stacks/php
<Directory /usr/share/stacks/php>
DirectoryIndex index.php
AllowOverride None
order deny,allow
deny from all
# This for local browsing only
# allow from 127.0.0.0/255.0.0.0 ::1/128
# Or switch to this for global visibility
allow from all
<IfModule mod_php5.c>
php_flag magic_quotes_gpc Off
#php_flag track_vars On
#php_value include_path .
</IfModule>
<IfModule !mod_php5.c>
<IfModule mod_actions.c>
<IfModule mod_cgi.c>
AddType application/x-httpd-php .php
Action application/x-httpd-php /cgi-bin/php
</IfModule>
<IfModule mod_cgid.c>
AddType application/x-httpd-php .php
Action application/x-httpd-php /cgi-bin/php
</IfModule>
</IfModule>
</IfModule>
</Directory>
debian/changelog
View file @ aeb8b8b5
stacks (2.41+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
* debhelper 12
* Standards-Version: 4.4.0
* Secure URI in copyright format
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* dh_auto_install --no-parallel
* Removed stacks-web package since the code for the web service
was removed from upstream source and the package has no active
users according to popcon anyway
-- Andreas Tille <tille@debian.org> Wed, 10 Jul 2019 21:58:30 +0200
stacks (2.2+dfsg-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ aeb8b8b5
......@@ -4,14 +4,14 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
Build-Depends: debhelper (>= 12~),
python,
zlib1g-dev,
libbam-dev,
libsparsehash-dev (>= 2.0),
libsparsehash-dev,
samtools,
libhts-dev
Standards-Version: 4.2.1
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/stacks
Vcs-Git: https://salsa.debian.org/med-team/stacks.git
Homepage: http://creskolab.uoregon.edu/stacks/
......@@ -24,6 +24,9 @@ Depends: ${shlibs:Depends},
samtools,
libdbi-perl
Recommends: libspreadsheet-writeexcel-perl
Conflicts: stacks-web
Provides: stacks-web
Replaces: stacks-web
Description: pipeline for building loci from short-read DNA sequences
Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
......@@ -32,22 +35,3 @@ Description: pipeline for building loci from short-read DNA sequences
.
Note that this package installs Stacks such that all commands must be run as:
$ stacks <cmdname> <args>
Package: stacks-web
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
apache2 | httpd,
default-mysql-server | virtual-mysql-server,
libapache2-mod-php | php-cgi,
libdbd-mysql-perl,
php-mdb2-driver-mysql
Recommends: stacks
Description: web interface for displaying loci from short-read sequences
Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
with restriction enzyme-based data, such as RAD-seq, for the purpose of
building genetic maps and conducting population genomics and phylogeography.
.
This package provides the web-based viewer which you can use to examine Stacks
output that has been loaded into a MySQL database.
debian/copyright
View file @ aeb8b8b5
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Stacks
Upstream-Contact: Julian Catchen <jcatchen@uoregon.edu>
Source: http://creskolab.uoregon.edu/stacks/
......
debian/patches/constants.php.patch deleted 100644 → 0
View file @ 1aaba5f8
Author: Tim Booth <tbooth@ceh.ac.uk>
Last-Update: Wed, 18 Feb 2015 11:34:22 +0000
Description: Work together width /usr/sbin/stacks-setup-database
See README.Debian
--- a/php/constants.php.dist
+++ b/php/constants.php.dist
@@ -21,8 +21,8 @@
//
// Credentials to access Stacks MySQL databases
//
-$db_user = "dbuser";
-$db_pass = "dbpass";
+$db_user = "stacksweb";
+$db_pass = "stacksweb";
$db_host = "localhost";
//